Starting phenix.real_space_refine on Thu Nov 16 22:15:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/11_2023/3j9p_6267.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11100 2.51 5 N 2844 2.21 5 O 2888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D GLU 1063": "OE1" <-> "OE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1063": "OE1" <-> "OE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1063": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "B" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Time building chain proxies: 8.81, per 1000 atoms: 0.52 Number of scatterers: 16952 At special positions: 0 Unit cell: (115.482, 115.482, 142.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2888 8.00 N 2844 7.00 C 11100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.2 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 65.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 467 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'D' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL D 564 " --> pdb=" O HIS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 602 " --> pdb=" O THR D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 627 Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS D 633 " --> pdb=" O TYR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 721 " --> pdb=" O ARG D 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 782 " --> pdb=" O PHE D 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE D 783 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR D 812 " --> pdb=" O GLU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA D 836 " --> pdb=" O TRP D 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG D 872 " --> pdb=" O LYS D 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 913 removed outlier: 4.276A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 929 Processing helix chain 'D' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA D 939 " --> pdb=" O VAL D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 970 removed outlier: 3.965A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D1049 " --> pdb=" O LEU D1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D1050 " --> pdb=" O LYS D1046 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS D1060 " --> pdb=" O PHE D1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D1071 " --> pdb=" O LEU D1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.977A pdb=" N PHE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 783 removed outlier: 3.547A pdb=" N ILE A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.695A pdb=" N ALA A 836 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 933 through 948 removed outlier: 4.003A pdb=" N ALA A 939 " --> pdb=" O VAL A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.975A pdb=" N PHE B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 522 removed outlier: 4.208A pdb=" N HIS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.741A pdb=" N LEU B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL B 564 " --> pdb=" O HIS B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 602 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 783 removed outlier: 3.546A pdb=" N ILE B 770 " --> pdb=" O ASN B 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 782 " --> pdb=" O PHE B 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 828 through 850 removed outlier: 3.696A pdb=" N ALA B 836 " --> pdb=" O TRP B 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 913 removed outlier: 4.277A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 Processing helix chain 'B' and resid 933 through 948 removed outlier: 4.002A pdb=" N ALA B 939 " --> pdb=" O VAL B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B1050 " --> pdb=" O LYS B1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B1060 " --> pdb=" O PHE B1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL C 564 " --> pdb=" O HIS C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 601 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 602 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS C 633 " --> pdb=" O TYR C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 721 " --> pdb=" O ARG C 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE C 770 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 782 " --> pdb=" O PHE C 778 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 783 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR C 812 " --> pdb=" O GLU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA C 836 " --> pdb=" O TRP C 832 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG C 872 " --> pdb=" O LYS C 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 929 Processing helix chain 'C' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA C 939 " --> pdb=" O VAL C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 970 removed outlier: 3.963A pdb=" N HIS C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR C1049 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C1050 " --> pdb=" O LYS C1046 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C1060 " --> pdb=" O PHE C1056 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C1071 " --> pdb=" O LEU C1067 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2661 1.32 - 1.44: 4574 1.44 - 1.57: 9837 1.57 - 1.69: 36 1.69 - 1.82: 196 Bond restraints: 17304 Sorted by residual: bond pdb=" CA VAL C 824 " pdb=" CB VAL C 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.82e+01 bond pdb=" CA VAL B 824 " pdb=" CB VAL B 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.81e+01 bond pdb=" CA VAL D 824 " pdb=" CB VAL D 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.80e+01 bond pdb=" CA VAL A 824 " pdb=" CB VAL A 824 " ideal model delta sigma weight residual 1.540 1.612 -0.071 1.36e-02 5.41e+03 2.76e+01 bond pdb=" CA LEU D 480 " pdb=" C LEU D 480 " ideal model delta sigma weight residual 1.524 1.578 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 17299 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.37: 352 105.37 - 112.82: 8895 112.82 - 120.27: 7308 120.27 - 127.72: 6733 127.72 - 135.17: 200 Bond angle restraints: 23488 Sorted by residual: angle pdb=" C GLU C 681 " pdb=" N PRO C 682 " pdb=" CA PRO C 682 " ideal model delta sigma weight residual 119.78 129.49 -9.71 1.03e+00 9.43e-01 8.89e+01 angle pdb=" C GLU D 681 " pdb=" N PRO D 682 " pdb=" CA PRO D 682 " ideal model delta sigma weight residual 119.78 129.47 -9.69 1.03e+00 9.43e-01 8.84e+01 angle pdb=" C GLU A 681 " pdb=" N PRO A 682 " pdb=" CA PRO A 682 " ideal model delta sigma weight residual 119.78 129.46 -9.68 1.03e+00 9.43e-01 8.83e+01 angle pdb=" C GLU B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.78 129.45 -9.67 1.03e+00 9.43e-01 8.81e+01 angle pdb=" N ASN A 766 " pdb=" CA ASN A 766 " pdb=" CB ASN A 766 " ideal model delta sigma weight residual 112.41 126.89 -14.48 1.55e+00 4.16e-01 8.73e+01 ... (remaining 23483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 9343 22.99 - 45.98: 729 45.98 - 68.97: 152 68.97 - 91.97: 20 91.97 - 114.96: 4 Dihedral angle restraints: 10248 sinusoidal: 3652 harmonic: 6596 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N SER A 613 " pdb=" CA SER A 613 " ideal model delta harmonic sigma weight residual -180.00 -65.04 -114.96 0 5.00e+00 4.00e-02 5.29e+02 dihedral pdb=" CA PHE B 612 " pdb=" C PHE B 612 " pdb=" N SER B 613 " pdb=" CA SER B 613 " ideal model delta harmonic sigma weight residual -180.00 -65.09 -114.91 0 5.00e+00 4.00e-02 5.28e+02 dihedral pdb=" CA PHE C 612 " pdb=" C PHE C 612 " pdb=" N SER C 613 " pdb=" CA SER C 613 " ideal model delta harmonic sigma weight residual -180.00 -65.12 -114.88 0 5.00e+00 4.00e-02 5.28e+02 ... (remaining 10245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2146 0.077 - 0.155: 580 0.155 - 0.232: 58 0.232 - 0.309: 16 0.309 - 0.386: 8 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA VAL A 824 " pdb=" N VAL A 824 " pdb=" C VAL A 824 " pdb=" CB VAL A 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL C 824 " pdb=" N VAL C 824 " pdb=" C VAL C 824 " pdb=" CB VAL C 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA VAL D 824 " pdb=" N VAL D 824 " pdb=" C VAL D 824 " pdb=" CB VAL D 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2805 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D1047 " -0.038 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" CD GLN D1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN D1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN D1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C1047 " -0.038 2.00e-02 2.50e+03 7.58e-02 5.75e+01 pdb=" CD GLN C1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN C1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN C1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B1047 " 0.038 2.00e-02 2.50e+03 7.55e-02 5.71e+01 pdb=" CD GLN B1047 " -0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN B1047 " 0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B1047 " 0.044 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 628 2.67 - 3.23: 18247 3.23 - 3.79: 25629 3.79 - 4.34: 31485 4.34 - 4.90: 48026 Nonbonded interactions: 124015 Sorted by model distance: nonbonded pdb=" O MET A1072 " pdb=" NH2 ARG B 458 " model vdw 2.113 2.520 nonbonded pdb=" O HIS C 970 " pdb=" ND1 HIS C 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS D 970 " pdb=" ND1 HIS D 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS B 970 " pdb=" ND1 HIS B 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS A 970 " pdb=" ND1 HIS A 970 " model vdw 2.123 2.520 ... (remaining 124010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.630 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.340 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 17304 Z= 0.573 Angle : 1.852 14.481 23488 Z= 1.228 Chirality : 0.070 0.386 2808 Planarity : 0.006 0.076 2888 Dihedral : 17.684 114.956 5952 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 1.64 % Allowed : 10.18 % Favored : 88.18 % Rotamer: Outliers : 4.64 % Allowed : 24.04 % Favored : 71.33 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.68 % Twisted Proline : 5.56 % Twisted General : 3.96 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.15), residues: 2200 helix: -1.89 (0.11), residues: 1412 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 443 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 20 residues processed: 492 average time/residue: 0.3032 time to fit residues: 217.8971 Evaluate side-chains 285 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1636 time to fit residues: 8.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 ASN ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN ** D1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 ASN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN B 570 HIS ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 GLN C 570 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN ** C1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.274 Angle : 0.999 12.811 23488 Z= 0.518 Chirality : 0.048 0.193 2808 Planarity : 0.004 0.032 2888 Dihedral : 7.972 45.214 2356 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.86 % Favored : 91.05 % Rotamer: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 4.10 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2200 helix: -0.62 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 374 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 374 average time/residue: 0.2489 time to fit residues: 146.4815 Evaluate side-chains 237 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 163 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17304 Z= 0.312 Angle : 0.951 11.453 23488 Z= 0.502 Chirality : 0.047 0.189 2808 Planarity : 0.005 0.038 2888 Dihedral : 7.098 31.302 2356 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.32 % Favored : 89.59 % Rotamer: Outliers : 0.24 % Allowed : 6.02 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2200 helix: -0.41 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -3.24 (0.19), residues: 800 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 283 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 287 average time/residue: 0.2595 time to fit residues: 116.3877 Evaluate side-chains 212 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17304 Z= 0.217 Angle : 0.884 11.365 23488 Z= 0.460 Chirality : 0.045 0.178 2808 Planarity : 0.005 0.040 2888 Dihedral : 6.414 32.559 2356 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.36 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2200 helix: -0.18 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -3.18 (0.21), residues: 776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2695 time to fit residues: 133.7074 Evaluate side-chains 239 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 149 optimal weight: 0.0980 chunk 0 optimal weight: 10.9990 chunk 110 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17304 Z= 0.232 Angle : 0.869 11.007 23488 Z= 0.452 Chirality : 0.044 0.188 2808 Planarity : 0.005 0.045 2888 Dihedral : 6.117 33.392 2356 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.23 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2200 helix: -0.23 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -3.20 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2553 time to fit residues: 111.1398 Evaluate side-chains 217 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17304 Z= 0.286 Angle : 0.903 10.420 23488 Z= 0.469 Chirality : 0.045 0.181 2808 Planarity : 0.005 0.047 2888 Dihedral : 6.260 34.487 2356 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.95 % Favored : 88.50 % Rotamer: Outliers : 0.12 % Allowed : 2.71 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2200 helix: -0.24 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 265 average time/residue: 0.2767 time to fit residues: 114.0904 Evaluate side-chains 210 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1932 time to fit residues: 3.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 121 optimal weight: 0.0870 chunk 215 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 512 HIS ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.7741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17304 Z= 0.216 Angle : 0.862 10.792 23488 Z= 0.443 Chirality : 0.044 0.190 2808 Planarity : 0.004 0.048 2888 Dihedral : 5.920 33.217 2356 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.45 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2200 helix: -0.09 (0.13), residues: 1396 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2712 time to fit residues: 120.5771 Evaluate side-chains 230 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 HIS ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17304 Z= 0.223 Angle : 0.878 10.853 23488 Z= 0.452 Chirality : 0.044 0.222 2808 Planarity : 0.005 0.051 2888 Dihedral : 5.837 32.713 2356 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.95 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2200 helix: -0.11 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2675 time to fit residues: 118.0809 Evaluate side-chains 228 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.8071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17304 Z= 0.227 Angle : 0.899 10.831 23488 Z= 0.464 Chirality : 0.044 0.210 2808 Planarity : 0.005 0.049 2888 Dihedral : 5.824 32.147 2356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.27 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2200 helix: -0.11 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -2.95 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2843 time to fit residues: 126.7358 Evaluate side-chains 217 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 205 optimal weight: 0.3980 chunk 177 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN C 512 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17304 Z= 0.219 Angle : 0.924 11.067 23488 Z= 0.471 Chirality : 0.045 0.227 2808 Planarity : 0.005 0.050 2888 Dihedral : 5.723 31.184 2356 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.09 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 2200 helix: -0.17 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -2.89 (0.22), residues: 800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2766 time to fit residues: 122.2524 Evaluate side-chains 218 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 chunk 177 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 940 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.035082 restraints weight = 121060.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.036137 restraints weight = 87898.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036906 restraints weight = 67476.229| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17304 Z= 0.219 Angle : 0.910 12.654 23488 Z= 0.465 Chirality : 0.044 0.236 2808 Planarity : 0.005 0.050 2888 Dihedral : 5.671 31.524 2356 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.41 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 2200 helix: -0.18 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 796 =============================================================================== Job complete usr+sys time: 3300.49 seconds wall clock time: 61 minutes 17.49 seconds (3677.49 seconds total)